HEADER HYDROLASE 19-JAN-09 3FWX TITLE THE CRYSTAL STRUCTURE OF THE PEPTIDE DEFORMYLASE FROM VIBRIO CHOLERAE TITLE 2 O1 BIOVAR EL TOR STR. N16961 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE O395; SOURCE 3 ORGANISM_TAXID: 345073; SOURCE 4 STRAIN: STR. N16961; SOURCE 5 GENE: DEF-1, GI:15640078, VC0395_A2473; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG19C KEYWDS PEPTIDE DEFORMYLASE, STRUCTURAL GENOMICS, CSGID, HYDROLASE, NIAID KEYWDS 2 STRUCTURAL GENOMICS, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS KEYWDS 3 DISEASES EXPDTA X-RAY DIFFRACTION AUTHOR R.ZHANG,M.ZHOU,J.STAM,W.ANDERSON,A.JOACHIMIAK,CENTER FOR STRUCTURAL AUTHOR 2 GENOMICS OF INFECTIOUS DISEASES (CSGID) REVDAT 3 13-JUL-11 3FWX 1 VERSN REVDAT 2 05-MAY-09 3FWX 1 REMARK REVDAT 1 17-MAR-09 3FWX 0 JRNL AUTH R.ZHANG,M.ZHOU,J.STAM,W.ANDERSON,A.JOACHIMIAK JRNL TITL THE CRYSTAL STRUCTURE OF THE PEPTIDE DEFORMYLASE FROM VIBRIO JRNL TITL 2 CHOLERAE O1 BIOVAR EL TOR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0054 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 105.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.900 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 25897 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1368 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1929 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2270 REMARK 3 BIN FREE R VALUE SET COUNT : 106 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2620 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 289 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 22.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.35000 REMARK 3 B22 (A**2) : 0.40000 REMARK 3 B33 (A**2) : -0.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.187 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.180 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.119 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.186 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2654 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1820 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3592 ; 1.922 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4468 ; 1.116 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 328 ; 6.149 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 132 ;37.085 ;25.152 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 500 ;15.286 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;17.116 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 422 ; 0.150 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2922 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 476 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1648 ; 1.102 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 658 ; 0.347 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2684 ; 1.904 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1006 ; 3.328 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 908 ; 5.417 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 3 A 50 REMARK 3 RESIDUE RANGE : A 51 A 100 REMARK 3 RESIDUE RANGE : A 101 A 167 REMARK 3 ORIGIN FOR THE GROUP (A): 26.9350 4.3410 71.0510 REMARK 3 T TENSOR REMARK 3 T11: 0.0455 T22: 0.0618 REMARK 3 T33: 0.1005 T12: 0.0108 REMARK 3 T13: -0.0389 T23: -0.0094 REMARK 3 L TENSOR REMARK 3 L11: 0.4007 L22: 0.5936 REMARK 3 L33: 1.6442 L12: 0.2154 REMARK 3 L13: -0.5685 L23: -0.2463 REMARK 3 S TENSOR REMARK 3 S11: 0.0455 S12: -0.0356 S13: -0.0080 REMARK 3 S21: 0.0932 S22: -0.0267 S23: -0.0411 REMARK 3 S31: -0.0171 S32: 0.1572 S33: -0.0188 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 3 B 50 REMARK 3 RESIDUE RANGE : B 51 B 100 REMARK 3 RESIDUE RANGE : B 101 B 167 REMARK 3 ORIGIN FOR THE GROUP (A): 56.9050 3.6750 86.7600 REMARK 3 T TENSOR REMARK 3 T11: 0.1127 T22: 0.0327 REMARK 3 T33: 0.1240 T12: 0.0131 REMARK 3 T13: -0.0089 T23: -0.0371 REMARK 3 L TENSOR REMARK 3 L11: 0.6567 L22: 0.3427 REMARK 3 L33: 1.6646 L12: 0.2135 REMARK 3 L13: -0.2930 L23: -0.6620 REMARK 3 S TENSOR REMARK 3 S11: -0.0212 S12: 0.0951 S13: -0.0379 REMARK 3 S21: -0.0469 S22: 0.0485 S23: -0.0083 REMARK 3 S31: 0.1802 S32: -0.0117 S33: -0.0273 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3FWX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JAN-09. REMARK 100 THE RCSB ID CODE IS RCSB051144. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL3000 REMARK 200 DATA SCALING SOFTWARE : HKL3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25897 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 105.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.7200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.70 REMARK 200 R MERGE FOR SHELL (I) : 0.66100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: HKL3000_SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10MM SODIUM CITRATE, 33% PEG 6000, PH REMARK 280 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 105.17150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 105.17150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 30.65250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.72800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.65250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.72800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 105.17150 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.65250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 30.72800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 105.17150 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.65250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 30.72800 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 314 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MSE A 1 REMARK 465 SER A 2 REMARK 465 LYS A 168 REMARK 465 LYS A 169 REMARK 465 MSE B 1 REMARK 465 SER B 2 REMARK 465 LYS B 168 REMARK 465 LYS B 169 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH2 ARG B 82 OG1 THR B 108 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A 40 CZ TYR A 40 CE2 0.080 REMARK 500 VAL A 101 CB VAL A 101 CG2 0.138 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 67 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 164 CG - CD - NE ANGL. DEV. = -13.6 DEGREES REMARK 500 ARG A 164 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 164 NE - CZ - NH2 ANGL. DEV. = -6.7 DEGREES REMARK 500 ARG B 67 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG B 67 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG B 82 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG B 82 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO A 10 34.02 -93.36 REMARK 500 HIS A 55 57.52 -97.35 REMARK 500 ASP A 125 -136.74 54.13 REMARK 500 PRO B 10 36.11 -94.17 REMARK 500 HIS B 55 57.44 -96.72 REMARK 500 ASP B 125 -132.53 52.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 234 DISTANCE = 5.70 ANGSTROMS REMARK 525 HOH B 228 DISTANCE = 5.51 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 170 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 91 SG REMARK 620 2 HIS A 133 NE2 106.4 REMARK 620 3 HIS A 137 NE2 101.7 118.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 170 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 91 SG REMARK 620 2 HIS B 133 NE2 114.2 REMARK 620 3 HIS B 137 NE2 101.6 115.9 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 170 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 170 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: IDP01357 RELATED DB: TARGETDB DBREF 3FWX A 1 169 UNP A5F4B3 A5F4B3_VIBC3 1 169 DBREF 3FWX B 1 169 UNP A5F4B3 A5F4B3_VIBC3 1 169 SEQRES 1 A 169 MSE SER VAL LEU GLN VAL LEU THR PHE PRO ASP ASP ARG SEQRES 2 A 169 LEU ARG THR VAL ALA LYS PRO VAL GLU GLN VAL THR PRO SEQRES 3 A 169 GLU ILE GLN GLN ILE VAL ASP ASP MSE LEU GLU THR MSE SEQRES 4 A 169 TYR ALA GLU GLU GLY ILE GLY LEU ALA ALA THR GLN VAL SEQRES 5 A 169 ASP ILE HIS GLN ARG ILE VAL VAL ILE ASP ILE SER GLU SEQRES 6 A 169 THR ARG ASP GLN PRO MSE VAL LEU ILE ASN PRO GLU ILE SEQRES 7 A 169 ILE GLU LYS ARG GLY GLU ASP GLY ILE GLU GLU GLY CYS SEQRES 8 A 169 LEU SER VAL PRO GLY ALA ARG ALA LEU VAL PRO ARG ALA SEQRES 9 A 169 ALA GLU VAL THR VAL LYS ALA LEU ASP ARG ASN GLY GLN SEQRES 10 A 169 GLU TYR GLN PHE ASP ALA ASP ASP LEU LEU ALA ILE CYS SEQRES 11 A 169 VAL GLN HIS GLU LEU ASP HIS LEU ALA GLY LYS LEU PHE SEQRES 12 A 169 VAL ASP TYR LEU SER PRO LEU LYS ARG ASN ARG ILE LYS SEQRES 13 A 169 GLU LYS LEU GLU LYS ILE LYS ARG PHE ASN GLU LYS LYS SEQRES 1 B 169 MSE SER VAL LEU GLN VAL LEU THR PHE PRO ASP ASP ARG SEQRES 2 B 169 LEU ARG THR VAL ALA LYS PRO VAL GLU GLN VAL THR PRO SEQRES 3 B 169 GLU ILE GLN GLN ILE VAL ASP ASP MSE LEU GLU THR MSE SEQRES 4 B 169 TYR ALA GLU GLU GLY ILE GLY LEU ALA ALA THR GLN VAL SEQRES 5 B 169 ASP ILE HIS GLN ARG ILE VAL VAL ILE ASP ILE SER GLU SEQRES 6 B 169 THR ARG ASP GLN PRO MSE VAL LEU ILE ASN PRO GLU ILE SEQRES 7 B 169 ILE GLU LYS ARG GLY GLU ASP GLY ILE GLU GLU GLY CYS SEQRES 8 B 169 LEU SER VAL PRO GLY ALA ARG ALA LEU VAL PRO ARG ALA SEQRES 9 B 169 ALA GLU VAL THR VAL LYS ALA LEU ASP ARG ASN GLY GLN SEQRES 10 B 169 GLU TYR GLN PHE ASP ALA ASP ASP LEU LEU ALA ILE CYS SEQRES 11 B 169 VAL GLN HIS GLU LEU ASP HIS LEU ALA GLY LYS LEU PHE SEQRES 12 B 169 VAL ASP TYR LEU SER PRO LEU LYS ARG ASN ARG ILE LYS SEQRES 13 B 169 GLU LYS LEU GLU LYS ILE LYS ARG PHE ASN GLU LYS LYS MODRES 3FWX MSE A 35 MET SELENOMETHIONINE MODRES 3FWX MSE A 39 MET SELENOMETHIONINE MODRES 3FWX MSE A 71 MET SELENOMETHIONINE MODRES 3FWX MSE B 35 MET SELENOMETHIONINE MODRES 3FWX MSE B 39 MET SELENOMETHIONINE MODRES 3FWX MSE B 71 MET SELENOMETHIONINE HET MSE A 35 8 HET MSE A 39 8 HET MSE A 71 8 HET MSE B 35 8 HET MSE B 39 8 HET MSE B 71 8 HET ZN A 170 1 HET ZN B 170 1 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 3 ZN 2(ZN 2+) FORMUL 5 HOH *289(H2 O) HELIX 1 1 ASP A 11 THR A 16 5 6 HELIX 2 2 THR A 25 GLU A 42 1 18 HELIX 3 3 THR A 50 ASP A 53 5 4 HELIX 4 4 ASP A 124 ALA A 139 1 16 HELIX 5 5 LEU A 142 LEU A 147 5 6 HELIX 6 6 SER A 148 ARG A 164 1 17 HELIX 7 7 ASP B 11 THR B 16 5 6 HELIX 8 8 THR B 25 GLU B 42 1 18 HELIX 9 9 THR B 50 ASP B 53 5 4 HELIX 10 10 ASP B 125 ALA B 139 1 15 HELIX 11 11 LEU B 142 LEU B 147 5 6 HELIX 12 12 SER B 148 ARG B 164 1 17 SHEET 1 A 5 GLY A 46 ALA A 48 0 SHEET 2 A 5 ILE A 58 ILE A 61 -1 O VAL A 60 N LEU A 47 SHEET 3 A 5 MSE A 71 ARG A 82 -1 O LEU A 73 N VAL A 59 SHEET 4 A 5 GLU A 106 LEU A 112 -1 O THR A 108 N ILE A 79 SHEET 5 A 5 GLU A 118 ALA A 123 -1 O TYR A 119 N ALA A 111 SHEET 1 B 2 ASP A 85 GLU A 89 0 SHEET 2 B 2 ALA A 99 ARG A 103 -1 O ARG A 103 N ASP A 85 SHEET 1 C 5 GLY B 46 ALA B 48 0 SHEET 2 C 5 ILE B 58 ILE B 61 -1 O VAL B 60 N LEU B 47 SHEET 3 C 5 MSE B 71 ARG B 82 -1 O LEU B 73 N VAL B 59 SHEET 4 C 5 GLU B 106 LEU B 112 -1 O THR B 108 N ILE B 79 SHEET 5 C 5 GLU B 118 ASP B 124 -1 O TYR B 119 N ALA B 111 SHEET 1 D 2 ASP B 85 GLU B 89 0 SHEET 2 D 2 ALA B 99 ARG B 103 -1 O ARG B 103 N ASP B 85 LINK C ASP A 34 N MSE A 35 1555 1555 1.33 LINK C MSE A 35 N LEU A 36 1555 1555 1.33 LINK C THR A 38 N MSE A 39 1555 1555 1.34 LINK C MSE A 39 N TYR A 40 1555 1555 1.33 LINK C PRO A 70 N MSE A 71 1555 1555 1.32 LINK C MSE A 71 N VAL A 72 1555 1555 1.32 LINK C ASP B 34 N MSE B 35 1555 1555 1.33 LINK C MSE B 35 N LEU B 36 1555 1555 1.33 LINK C THR B 38 N MSE B 39 1555 1555 1.32 LINK C MSE B 39 N TYR B 40 1555 1555 1.33 LINK C PRO B 70 N MSE B 71 1555 1555 1.33 LINK C MSE B 71 N VAL B 72 1555 1555 1.33 LINK SG CYS A 91 ZN ZN A 170 1555 1555 2.53 LINK NE2 HIS A 133 ZN ZN A 170 1555 1555 2.17 LINK NE2 HIS A 137 ZN ZN A 170 1555 1555 1.95 LINK SG CYS B 91 ZN ZN B 170 1555 1555 2.46 LINK NE2 HIS B 133 ZN ZN B 170 1555 1555 2.16 LINK NE2 HIS B 137 ZN ZN B 170 1555 1555 2.07 CISPEP 1 PHE A 9 PRO A 10 0 7.85 CISPEP 2 PHE B 9 PRO B 10 0 7.52 SITE 1 AC1 4 GLN B 51 CYS B 91 HIS B 133 HIS B 137 SITE 1 AC2 4 GLN A 51 CYS A 91 HIS A 133 HIS A 137 CRYST1 61.305 61.456 210.343 90.00 90.00 90.00 C 2 2 21 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016312 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016272 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004754 0.00000